NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3510937 Query DataSets for GSM3510937
Status Public on Dec 11, 2021
Title Retina 3
Sample type SRA
 
Source name Retina
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Retinal ganglion cells
age: 3 months
Extracted molecule total RNA
Extraction protocol Retinae were dissociated into single cells. GFP+ cells were enriched by FACS sorting. The number and viability of sorted retinal cells were quantified using the Countess II (ThermoFisher AMQAX1000). Next, single cell libraries were generated with the Chromium Single Cell 3’ V2 Chemistry Library Kit, Gel Bead & Multiplex Kit and Chip Kit from 10X Genomics.
To generate the libraries, Enzymatic Fragmentation, End Repair and A-tailing Double Sided Size Selection were used to incorporate the barcodes and index read sequences. The libraries were qualified by bioanalyzer (Agilent Technologies) and quantified by a Qubit® dsDNA High Sensitivity Assay Kit (Invitrogen), then sequenced on Illumina Xten platform in 150 Paired-end configuration.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Raw reads were processed using the 10x Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with the mm10 as the reference. Cell Ranger can cluster the single cells, identify the marker genes of each cluster, and export a matrix with UMI values of each gene in a single cell. In total 468,282,957 reads were mapped and 3,237 cells were detected with a sequencing saturation of 86.2%. The R software package Seurat (https://satijalab.org/seurat, version 2.2) was used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: RGC_Matrix_all_cells.csv
Supplementary_files_format_and_content: barcodes.tsv
Supplementary_files_format_and_content: filtered_gene_bc_matrices_h5.h5
Supplementary_files_format_and_content: genes.tsv
 
Submission date Dec 13, 2018
Last update date Dec 11, 2021
Contact name Kangxin Jin
E-mail(s) kxjin@yahoo.com
Organization name Sun Yat-sen University
Department Zhongshan Ophthalmic Center
Street address 7 Jinsui Rd
City Guangzhou
State/province Guangdong Province
ZIP/Postal code 510510
Country China
 
Platform ID GPL21273
Series (1)
GSE123758 Diverse mammalian retinal ganglion cell types revealed by single cell transcriptome profiling
Relations
BioSample SAMN10587694
SRA SRX5127999

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap